Bis-biotinylation tags

ABSTRACT

Multi-biotinylated reactants are provided which can be used in divalent complexes for various applications such as colocalization, labeling, immobilization, and purification. Methods for constructing, purifying, and using the bis-biotinylated reactants are also provided. In certain embodiments, two bis-biotinylated reactants are bound to a single streptavidin tetramer to provide a complex having a 1:1 stoichiometry with respect to the bis-biotinylated reactants.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application No.61/835,311, filed Jun. 14, 2013, the full disclosure of which isincorporated herein by reference in its entirety for all purposes.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH

Not Applicable.

DESCRIPTION OF THE BACKGROUND ART

A common task in molecular biology is to identify and quantify thepresence of a protein in a complex mixture. For example, to identify thelevel of expression of a protein of interest, a western blot can beperformed in which a protein extract is run on a gel and stained withantibodies against a defined epitope of the protein of interest. Thedefined epitope can be a particular sequence or structure found in thenative protein, or can be a tag introduced during cloning, e.g, a “FLAGtag” for which specific antibodies are commercially available. Asecondary peroxidase-conjugated antibody specific for the primaryantibody bound to the protein is used to generate a detectable signal.This process is cumbersome and more streamlined methods for purificationof proteins from cell extracts are desirable.

Attaching optical labels to proteins can be an alternate strategy fordetection and quantification, however, this typically requires chemicalmodification of residues within the protein. Attaching dyes throughlysine or cysteine residues often modifies activity or reducessolubility making purification of the labeled protein difficult orimpossible. Fluorescent protein tags are available with a wide varietyof spectral properties, e.g., as described in Shaner, et al. (2005)Nature Methods 2(12):905-909, incorporated by reference herein in itsentirety for all purposes, but these tags are suboptimal forsingle-molecule experimentation.

The ability to synthesize DNA chemically has made possible theconstruction of peptides and proteins not otherwise found in nature anduseful in a wide variety of methods that would otherwise be verydifficult or impossible to perform. The patent literature, for instance,is replete with publications describing the recombinant expression ofreceptor proteins. See, e.g., PCT Patent Pub. No. 91/18982 and U.S. Pat.Nos. 5,081,228 and 4,968,607, which describe recombinant DNA moleculesencoding the IL-1 receptor; U.S. Pat. Nos. 4,816,565; 4,578,335; and4,845,198, which describe recombinant DNA and proteins relating to theIL-2 receptor; PCT Patent Pub. No. 91/08214, which describes EGFreceptor gene related nucleic acids; PCT Patent Pub. No. 91/16431 andU.S. Pat. No. 4,897,264, which describe the interferon gamma receptorand related proteins and nucleic acids; European Patent Office (EPO)Pub. No. 377,489, which describes the C5a receptor protein; PCT PatentPub. No. 90/08822, which describes the EPO receptor and related nucleicacids; PCT Patent Pub. No. 92/01715, which describes MHC receptors; andU.S. patent application Ser. No. 947,339, filed on Sep. 18, 1992, whichdescribes how HPAP-containing receptors can be cleaved from the cellsurface and how the anchoring sequences that remain can serve asrecognition sequences for antibodies that are used to immobilize thereceptor. Several of these publications, each of which is incorporatedherein by reference for all purposes, describe both how to isolate aparticular receptor protein (or the gene encoding the protein) andvariants of the receptor that may be useful in ways the natural ornative receptor is not.

The advances made with respect to receptor cloning and expression havebeen accompanied by advances in technology relating to methods forscreening a receptor against compounds that may interact with thereceptor in a desired fashion. One such advance relates to thegeneration of large numbers of compounds, or potential ligands, in avariety of random and semi-random “peptide diversity” generationsystems. These systems include the “peptides on plasmids” systemdescribed in U.S. Pat. No. 5,338,665, which is a continuation-in-part ofU.S. Pat. No. 5,270,170; the “peptides on phage” system described inU.S. patent application Ser. No. 718,577, filed Jun. 20, 1991, which isa continuation-in-part of Ser. No. 541,108, filed Jun. 20, 1990; Cwirlaet al., August 1990, Proc. Natl. Acad. Sci. USA 87: 6378-6382; Barrettet al., 1992, Analyt. Biochem. 204: 357-364; and PCT Patent Pub. Nos.91/18980 and 91/19818; the phage-based antibody display systemsdescribed in U.S. patent application Ser. No. 517,659, filed May 11,1990, and PCT Patent Pub. No. 91/17271; the bead-based systems forgenerating and screening nucleic acid ligands described in PCT Pub. Nos.91/19813, 92/05258, and 92/14843; the bead-based system described inU.S. patent application Ser. No. 946,239, filed Sep. 16, 1992, which isa continuation-in-part of Ser. No. 762,522, filed Sep. 18, 1991; and the“very large scaled immobilized polymer synthesis” system described inU.S. Pat. No. 5,143,854; PCT Patent Pub. Nos. 90/15070 and 92/10092,U.S. patent application Ser. No. 624,120, filed Dec. 6, 1990; Fodor etal., Feb. 15, 1991, Science 251: 767-773; Dower and Fodor, 1991, Ann.Rep. Med. Chem. 26:271-180; and U.S. patent application Ser. No.805,727, filed Dec. 6, 1991. Each of the above references isincorporated herein by reference for all purposes.

Other developments relate to how the receptor is used in such screeningmethods. One important advance relates to the development of reagentsand methods for immobilizing one or more receptors in a spatiallydefined array, as described in PCT Patent Pub. No. 91/07087, whichdescribes attachment of a receptor to avidin and subsequentimmobilization on a surface that bears biotin groups. Once theavidinylated receptor is bound to the biotin groups on the surface, thesurface can be used in screening compounds against the receptor.

Biotin is a cofactor that is covalently attached to several enzymesinvolved in the transfer of activated carboxyl groups. Biotin labelingof molecules not normally biotinylated can be used to label, detect,purify, and/or immobilize such molecules. These methods also rely uponthe proteins avidin and/or streptavidin, which bind very tightly andspecifically to biotin. Typically, the biotinylated molecules used insuch methods are prepared by an in vitro biotinylation process.Alternatively, methods for biotinylating proteins synthesized byrecombinant DNA techniques in vivo eliminates the need to chemicallybiotinylate these proteins after purification and greatly simplifies thepurification process, due to the ability to use the biotin as anaffinity tag (see Green, 1975, Adv. Protein Res. 29:85-133, incorporatedherein by reference).

Biotin-streptavidin interactions can also be used for linking differentmolecules together to form useful complexes. For example, sincestreptavidin has four binding sites for biotin, four biotin-labeledmolecules can be linked to a single streptavidin molecule. Certainspecific examples of methods comprising linkage of biotin-labeledmolecules through a streptavidin molecule are described in detail in theart, e.g., in U.S. patent application Ser. No. 13/767,619, filed Feb.14, 2013; U.S. Pat. Nos. 8,389,676; and 8,252,910, all of which areincorporated herein by reference in their entireties for all purposes.However, for some applications it is useful to generate a strong 1:1complex of two molecules, and this can be difficult with streptavidindue to its tetravalent nature. Many different stoichiometries can begenerated, e.g., 1:3 and 3:1. Methods have been previously described forcreating streptavidin tetramers with reduced numbers of active sites,e.g., in Howarth, et al, (2006) Nature Methods 3(4):267-73, which isincorporated herein by reference in its entirety for all purposes.However, the methods of Howarth involve mixing of two species ofrecombinant streptavidin and are cumbersome.

SUMMARY OF THE INVENTION

The present invention provides useful compounds, reagents, methods, andkits for biotinylating molecules and linking biotinylated moleculestogether via biotin-binding agents, such as streptavidin. The inventionprovides compositions comprising bis-biotinylated reactants, as well assuch bis-biotinylated reactants bound to a biotin-binding agent, e.g.,streptavidin. In preferred embodiments, the bis-biotin tag is bound to astreptavidin or other biotin-binding agent such that the bis-biotin tagbinds to two biotin-binding sites on a dimer of the streptavidintetramer.

In certain aspects, the invention provides a composition comprising afirst reactant coupled, preferably covalently coupled, to a firstbis-biotin tag. In various alternative embodiments, the first reactantis a protein, label, immobilization tag, purification tag, barcode, or asolid support. In more specific embodiments, the protein is an enzyme,e.g., a polymerase; the label is a fluorescent label, spin label, ormagnetic label; and the solid support is a bead or planar support, e.g.,an arrayed support. The bis-biotin tag is optionally tandemly orientedor configured on a branched linker. In some preferred embodiments,biotins in a bis-biotin tag are separated by 20-60 angstroms.Optionally, the composition further comprises a streptavidin tetramerbound to the first bis-biotin tag, e.g., wherein both biotin moieties inthe first bis-biotin tag are bound to the streptavidin tetramer, e.g.,both are bound to one of the two dimers in the streptavidin tetramer. Insome embodiments, the composition further comprises a streptavidintetramer bound to both the first bis-biotin tag and a second bis-biotintag. The second bis-biotin tag is typically covalently linked to asecond reactant. The two biotin moieties in the second bis-biotin tagare preferably both bound to the dimer of the streptavidin tetramer thatis not bound to the first bis-biotin tag.

In some aspects, the invention provides a method for colocalizing tworeactants, preferably in a 1:1 stoichiometry. In certain embodiments,such an embodiment comprises (a) linking, preferably covalently linking,a first of the reactants to a first bis-biotin tag; (b) linking,preferably covalently linking, a second of the reactants to a secondbis-biotin tag; (c) binding the first reactant to a tetravalentbiotin-binding agent, thereby producing a first complex comprising thefirst reactant bound to the tetravalent biotin-binding agent; and (d)exposing the second reactant to the first complex, thereby producing asecond complex comprising the second reactant bound to the firstcomplex. Optionally, the method further comprises isolating the firstcomplex prior to said exposing the second reactant and/or isolating thesecond complex. In some embodiments, the first reactant is a firstmember of a divalent binding pair, and the second reactant is a secondmember of a divalent binding pair, and further wherein production of thesecond complex increases binding between the first reactant and thesecond reactant. In specific embodiments, the first reactant is anenzyme and the second reactant is a substrate for the enzyme, andproduction of the second complex increases catalysis between the enzymeand the substrate. In further specific embodiments, the first reactantis a solid support and the second reactant is a molecule or molecularcomplex of interest, and production of the second complex immobilizesthe molecule or molecular complex of interest. In yet furtherembodiments, the first reactant is a detectable label for detecting thesecond reactant, and the complex serves to link the label to the secondreactant for use in a subsequent detection step. In alternativeembodiments, the first reactant is an immobilization tag forimmobilizing the second reactant, and the complex serves to link theimmobilization tag to the second reactant for use in a subsequentimmobilization step. In additional embodiments, the first reactant is apurification tag for isolating the second reactant, and the complexserves to link the purification tag to the second reactant for use in asubsequent isolation step.

In other aspects, the invention provides a labeling reagent comprising amulti-biotinylated detectable label and a tetravalent biotin-bindingagent. In preferred embodiments, the multi-biotinylated detectable labelcomprises a bis-biotin tag. Different types of detectable labels can beused, e.g., fluorescent dyes, a spin labels, quantum dots, etc. Thetetravalent biotin-binding agent is preferably a streptavidin tetramer.

In yet further aspects, the invention provides a composition comprisinga multi-biotinylated reactant comprising multiple biotin moieties,wherein all of the biotin moieties are bound to a single multivalentbiotin-binding agent. In certain embodiments, the multivalentbiotin-binding agent is a streptavidin tetramer, e.g., having all itsbiotin-binding sites occupied. The tetramer is optionally bound to asecond biotinylated reactant that is not the multi-biotinylatedreactant. Preferably, the biotin moieties are covalently bound to one orboth of the multi-biotinylated reactant and the second biotinylatedreactant. In certain embodiments, each of the multi-biotinylatedreactant and the second biotinylated reactant comprise a bis-biotin tag.In specific embodiments, the multivalent biotin-binding agent is astreptavidin tetramer, a first bis-biotin tag on the multi-biotinylatedreactant occupies both biotin-binding sites on a first dimer of thestreptavidin tetramer, and a second his-biotin tag on the secondbiotinylated reactant occupies both biotin-binding sites on a seconddimer of the streptavidin tetramer. The multi-biotinylated reactant canoptionally be a biotinylated fusion protein having at least twobiotinylation peptides, e.g. where the biotinylation peptides are in anN-terminal or C-terminal region of the fusion protein. The biotinylationpeptides can be tandemly arranged, or provided in a branchedconfiguration.

In summary, this invention provides compositions and methods for linkingreactants together in a preferred stoichiometry, e.g., a one-to-onestoichiometry. The compositions and methods are useful for a variety ofpurposes, including, e.g., potentially wide commercial utility forresearch and diagnostic applications. For example, particular utility isfound for the linking of labels to reactants, and localizing tworeactants together, e.g., to enhance a desired interaction.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 illustrates a tetrameric complex comprising two binding sitesblocked by a bis-biotinylated reactant and two binding sites availablefor further binding.

FIG. 2 illustrates a labeling reagent comprising a bis-biotinylateddetectable label bound to a tetravalent streptavidin.

FIG. 3 provides an illustrative embodiment of colocalization of tworeactants (Reactant 1 and Reactant 2) by bis-biotinylating bothreactants and binding both, either simultaneously or sequentially, to atetravalent complex.

FIG. 4 provides an illustrative example of a method of using atetravalent complex to link two reactants together with a 1:1stoichiometry wherein one reactant is tris-biotinylated and the otherreactant is mono-biotinylated.

FIG. 5 provides an illustrative example of an embodiment of theinvention, wherein a bis-biotinylated protein of interest (Protein 1)binds to a streptavidin bound to a body-linked label while non-specificproteins remain unbound (Proteins 2, 3, and 4).

FIG. 6 illustrates an embodiment of a gel separation strategy forseparating different streptavidin tetramer complexes.

FIG. 7 provides an illustrative embodiment in which Protein 1 andProtein 2 are each bound via a bis-biotin linkage to a differentstreptavidin tetramer, each comprising a nucleic acid tag, Tag 1 and Tag2, respectively.

FIG. 8 provides an example of a typical chromatogram for fractionscollected from an ion exchange column.

FIG. 9 provides an image of an exemplary high-throughput polymerasescreening gel.

FIG. 10 provides an illustrative embodiment of a bis-biotin taggingstrategy in which four SpyTags are fused to a polymerase enzyme.

FIG. 11 provides an illustrative embodiment of a method of forming acomplex comprising bis-biotinylated dyes bound to streptavidinmolecules, which are bound to bis-biotinylated SpyCatcher peptidescovalently linked to a protein-SpyTag fusion.

DETAILED DESCRIPTION

I. Definitions

For purposes of understanding the present invention, the following termsare defined.

The terms “bis-biotin,” “bis-biotin tag,” “bis-Btag,” and “bis-biotinmoiety” can be used interchangeably and generally refer to twocovalently-linked biotins linked (optionally, covalently linked) to areactant of interest. In certain preferred embodiments, a reactant ofinterest comprises a sequence that is recognized by a biotin ligase,which catalyzes a covalent linkage between the sequence and a biotinmolecule. Such a sequence is generally referred to as a biotin ligaserecognition sequence. Each biotin ligase recognition sequence in areactant of interest can be covalently linked to a biotin moiety, so areactant having multiple biotin ligase recognition sequences can becovalently linked to multiple biotins. A region of a reactant having oneor more biotin ligase recognition sequences is generally referred to asa biotinylation region of the reactant. For example, a bis-biotin canrefer to two biotins bound to two biotinylation peptides within a fusionprotein reactant.

The term “biotinylation peptide” refers to an amino acid sequence whichprovides a biotinylatable sequence motif. Thus, a biotinylation peptideis a peptide that is capable of being biotinylated.

The term “biotinylation sequence” refers to a nucleic acid sequence thatencodes a biotinylation peptide. Thus, transcription and translation ofa biotinylation sequence generates a biotinylation peptide.

The term “biotinylation enzyme” refers to the class of enzymes known asbiotin protein ligases, or enzymes which biotinylate other proteins orpeptides.

The term “fusion protein” generally refers to a protein which is acomposite of two separate proteins which are normally not joinedtogether as a single protein. Fusion proteins may be prepared byrecombinant nucleic acid methods, i.e., as a result of transcription andtranslation of a gene fusion comprising a segment which encodes abiotinylation peptide and a segment which encodes one or moreheterologous proteins, or by chemical synthesis methods well known inthe art.

The term “host cell” refers to a eukaryotic or procaryotic cell or groupof cells that can be or has been transformed by a recombinant DNAvector. For purposes of the present invention, procaryotic host cellsare preferred.

The term “linker” or “spacer” refers to a molecule or group of molecules(such as a monomer or polymer) that connects two molecules and oftenserves to place the two molecules in a preferred configuration and/orlocalization, for example, so that the two molecules can have preferredinteractions, e.g., with two different molecules, or two differentlocations on a single molecule or molecular complex.

The term “multi-biotin tag” generally refers to a tag comprisingmultiple biotin moieties. For example, a bis-biotin tag is amulti-biotin tag having only two biotin moieties.

The term “peptide” refers to an oligomer in which the monomers are aminoacids (usually alpha-amino acids) joined together through amide bonds.Alternatively, a “peptide” can be referred to as a “polypeptide.”Peptides are more than two amino acid monomers long, but more often aremore than 5 to 10 amino acid monomers long and can be even longer than20 amino acids, although peptides longer than 20 amino acids are morelikely to be called “polypeptides.”

The term “protein” is well known in the art and usually refers to a verylarge polypeptide, or set of associated polypeptides, that has somebiological function. For purposes of the present invention the terms“peptide,” “polypeptide,” and “protein” are largely interchangeable aslibraries of all three types can be prepared using substantially similarmethodology.

The term “reactant” as used herein is intended to generally indicate amolecule or molecular complex of interest, e.g., a reaction component.For example, a reactant can be a component of a multi-component mixture(e.g., reaction mixture, buffer, etc.), whether or not the componentdirectly or indirectly participates in a chemical or biochemicalreaction. In certain preferred embodiments, a reactant of interest isbiotinylated to facilitate further manipulation and/or analysis. Areactant can be any molecule or molecular complex, including but notlimited to polypeptides, proteins, enzymes, nucleic acids (e.g.,oligonucleotides, DNA, RNA, DNA/RNA hybrids, nucleic acid derivatives,etc.), cofactors, small molecules (e.g., drugs), “non-reactive”components, optical labels (e.g., fluorescent dyes), etc.

The term “solid support” refers to a material having a rigid orsemi-rigid surface. Such materials will preferably take the form ofsmall beads, pellets, disks, chips, or wafers, although other forms maybe used. In some embodiments, at least one surface of the solid supportwill be substantially flat. In some embodiments, a solid support is aplanar surface comprising nano-scale apertures, e.g., zero-modewaveguides, which are described in the art, e.g., see U.S. Pat. Nos.7,056,661 and 7,315,019, which are incorporated herein by reference intheir entireties for all purposes.

The term “surface” refers to any generally two-dimensional structure ona solid substrate and may have steps, ridges, kinks, terraces, nanoscaleapertures, and the like without ceasing to be a surface.

The term “synthetic” refers to production by in vitro chemical orenzymatic synthesis.

II. Methods and Reagents of the Invention

The biotin-streptavidin linkage is one of the strongest non-covalentinteractions characterized to date. The four streptavidin monomers arearranged as a dimer of dimers. As such, up to four biotin-taggedmolecules (e.g., proteins, nucleic acids, small molecules, etc.) can belinked together via interaction of their respective biotin tags with asingle streptavidin tetraplex. Where the object is to link multipleidentical biotin-tagged molecules together, e.g., for purificationpurposes, this arrangement is acceptable. However, in some cases it isdesired or necessary to have different biotin-tagged molecules bound tothe same streptavidin molecule in a specific stoichiometry. For example,where one needs two of each type of biotin-tagged molecule bound to asingle streptavidin molecule, simply combining them together in thepresence of streptavidin will result in complexes having not only thedesired 2:2 stoichiometry, but also 1:3, 3:1, 4:0, and 0:4. If one alsotakes into account streptavidin complexes that do not have all fourbinding sites occupied, the simple mixing strategy could also generatecomplexes having stoichiometries of 0:0, 1:0, 0:1, 1:1, 1:2, 2:1, 2:0,0:2, 3:0, and 0:3, with the predominant stoichiometries influenced byreagent concentration and time. For example, a complex comprising onesingly-biotinylated reactant bound to one streptavidin tetramer can bethe predominant product when binding is performed with an excess of thestreptavidin. Yet further, the four binding sites complicateapplications in which the desired stoichiometry is actually 1:1. Theinventors of the instant invention have developed a strategy forutilizing the beneficial high affinity and tight binding of thebiotin-streptavidin interaction for creating complexes having a 1:1stoichiometry.

Becket, et al. (1999, Protein Science 8:921-929), and U.S. Pat. Nos.5,723,584, 5,874,239, 5,932,433, 6,265,552, and 8,389,676 (incorporatedherein by reference in their entireties for all purposes) describebiotinylation peptides, which are peptide sequences linked to a proteinof interest to provide sites for biotin labeling. Briefly, a sequence(“biotinylation sequence”) encoding a biotinylation peptide is clonedinto a DNA sequence encoding a protein of interest such that expressionresults in a fusion protein comprising the protein of interest linked tothe biotinylation peptide, the latter of which is recognizable by abiotinylation enzyme, e.g., E. coli BirA. As such, the fusion proteincan be biotinylated in vivo, and addition of the biotin can furtherfacilitate purification of the fusion protein from the cell culture. Theshort, biotinylation peptides, whether biotinylated in viva or in vitro,can be used for a wide variety of purposes, including purification,immobilization, labeling, and detection of the fusion proteins. A fewillustrative examples include: (1) labeling receptors with biotin at adefined site, so that the labeled receptor could be, for instance, boundto streptavidin to produce a tetravalent receptor to increase thesensitivity of binding assays, such as those described in U.S. Pat. No.5,143,854, and U.S. patent application Ser. No. 946,239, filed Sep. 16,1992, each of which is incorporated herein by reference; (2) labelingfusion proteins containing peptide leads from any screening program, sothat the labeled fusion proteins can be used to test binding of thepeptide to receptors in a monovalent format (by probing with labeledstreptavidin after binding occurs) or in a multivalent format (byprebinding the fusions to labeled streptavidin and then testing bindingto receptors or so that the peptides can be mobilized onstreptavidin-coated beads or in microtiter wells for probing withreceptors, such as protease enzymes, in solution; (3) labeling peptidesor proteins directly by growing cells in the presence of tritiatedbiotin—with a biotin auxotrophs the peptides could be labeled at a knownspecific activity to permit quantitative measurements of bindingactivity; (4) developing technology for doing enzymatic reactions onsurfaces by exposing libraries of variant immobilized sequences to BirA,biotin, and ATP, so that those peptides that were substrates would bebiotinylated and could be detected with labeled streptavidin; and (5)attaching biotin specifically to an enzyme such as a polymerase enzymeto allow for binding the enzyme to a surface, for example for singlemolecule sequencing, e.g., as described in U.S. Pat. No. 7,056,661 andU.S. patent application Ser. No. 12/414,191, each of which isincorporated herein by reference.

Biotin-binding agents are known in the art and can be used with themethods and compositions provided herein. In certain embodiments,strategies provided herein use multiple biotin tags for linking a singlereactant to a single streptavidin molecule. Streptavidin is abiotin-binding agent that has been cloned and studied extensively. See,for example, Argaraña, et al. (1986) Nucleic Acids Res. 14(4):1871-1882; Asian, et al. (2007) Journal of Biotechnology 128:213-225;Asian, et al. (2005) J. Proc. Natl. Acad. Sci. USA 102(24):8507-8512;Baugh, et al. (2010) Biochemistry 49:4568-4570; Gitlin, et al. (1988)Biochem. J. 256:279-282; Hendrickson, et al. (1989) Proc. Natl. Acad.Sci. USA 86:2190-2194; Hyster, et al. (2012) Science 338:500-503; Klumb,et al. (1998) Biochemistry 37(21):7657-63; Kurzban, et al. (1991) J.Biol. Chem. 266(22): 14470-14477; Matsumoto, et al. (2011) J.Biotechnology 152:37-42; Sano, et al. (1996) Annals of the New YorkAcademy of Sciences 799 (Enzyme Engineering XIII) pp. 383-390; Schmidt,et al. (1994) Journal of Chromatography A 676:337-345; Srisawat, et al.(2001) RNA 7:632-641; Tahiri-Alaoui, et al. (2002) Nucleic Acids Res.30(10):e45; Voss, et al. (1997) Protein Engineering 10(8):975-982; andWilbur, et al. (2004) Bioconjugate Chem. 15:1454-1463, all of which areincorporated herein by reference in their entireties for all purposes.Although many of the compositions, methods, examples, and applicationsdescribed herein comprise the use or inclusion of streptavidin, e.g.,for binding to biotinylated reactants, it will be understood that otherbiotin-binding agents (e.g., nucleic acids or other molecules ormolecular complexes) can also be used, e.g., avidin, deglycoslylatedavidin (NeutrAvidin), traptavidin, and variants, mutants, or derivativesthereof. For example, U.S. Pat. No. 7,981,632 describes the “strep-tag”peptide, which binds to a modified version of streptavidin, streptactin.The present invention contemplates using the reagents provided herein incombination with streptactin and/or the strep-tag. For example,streptactin can be substituted for streptavidin in applications wherebis-biotin moieties can be bound to streptactin instead of single biotinmoieties; alternatively, one or more strep-tag peptides can be linked toa reactant which is subsequently bound to streptactin, or tostreptavidin where binding is strong enough. Linking of strep-tags toreactants can be accomplished using conventional molecular biologytechniques, cloning, chemical synthesis, and the like. Yet further,peptide and nucleic acid aptamers having an affinity for streptavidinhave also been developed and described in the art, e.g., inTahiri-Alaoui, et al. (2002) Nuc. Ac. Res. 30(10):e45; and Wilson, etal. (2001) Proc. Natl. Acad. Sci. USA 98:3750-3755, both of which areincorporated herein by reference in their entireties for all purposes.Such streptavidin-binding aptamers can be linked to reactants tofacilitate binding to streptavidin in a manner similar to the biotintags described herein. For example, two linked aptamers on a singlereactant can operate in a manner similar to a bis-biotin tag and providea means of linking the reactant to two binding sites on a streptavidinmolecule. As such, recitation of streptavidin and biotin in variousembodiments herein is merely exemplary and in no way excludes the use ofother biotin- or streptavidin-binding reactants, either instead of or incombination with streptavidin and/or biotin, in the various aspects ofthe invention described herein, e.g., methods, compositions, and kits.As such, embodiments are contemplated that comprise differentcombinations of binding partners in the same complex, e.g., a reactanthaving a single biotin tag and a single streptavidin-binding aptamer,where the reactant binds to a streptavidin tetramer, with the aptamerbound to one binding site in one dimer of the tetramer, and the biotinbound to the other binding site in the same dimer.

Further, although various examples herein focus on binding a singlemulti-biotin tag to a reactant of interest, it will be understood that aplurality of multi-biotin tags can be linked to a single reactant, e.g.,where binding to multiple individual biotin-binding agents is desired.For example, where a single reactant comprises two bis-biotin tags, eachof the tags can bind to a different streptavidin, which can bind toother biotin-tagged reactants, e.g., other reactants, labels, solidsupports, etc. Networks of multi-biotinylated reactants linked to oneanother through binding to biotin-binding agents is contemplated, e.g.,for reconstituting catalytic pathways (e.g. metabolic or syntheticpathways), or for enhancing complex formation between multiple differentreactants (e.g., components in a macromolecular complex).

In certain preferred aspects of the instant invention, both biotins in abis-biotin tag (or the multiple biotins in a multi-biotin tag) areintended to all bind to the same biotin-binding agent, e.g.,streptavidin, traptavidin, etc., to provide a stable linkage between areactant to which the bis-biotin tag is covalently bound and thebiotin-binding agent. Whereas “bis-biotin linkers” are described byRingler and Schulz (2003) Science 302, 106-109 (incorporated herein byreference in its entirety for all purposes), they are used as a linkagebetween two different molecules, each of which has a biotin-bindingsite. In other words, the two biotins on the bis-biotin linker areintended to noncovalently bind to two different molecules, therebyconnecting them via the linker. As such, neither of the molecules iscovalently linked to the bis-biotin linker. Other multi-biotin linkers,termed “bintinylated starburst dendrimers,” are described in Wilbur, etal. (1998) Bioconjugate Chem. 9:813-825 and U.S. Pat. No. 7,141,676(incorporated herein by reference in their entireties for all purposes)for use in cancer pretargeting protocols. Once again, these dendrimersdid not comprise a covalent linkage to a reactant of interest, butrather noncovalently connected molecules in vivo. Additional bis-biotinlinkers are described by Wilbur, et al. (1997) Bioconjugate Chem.8:819-832 (incorporated herein by reference in its entirety for allpurposes); and although in some embodiments two biotins in atris-biotinylated linker both bound to the same streptavidin molecule,the third biotin bound to a different streptavidin molecule, e.g., inorder to form a molecular network of linkers and streptavidin tetramers.As such, not all biotins in the multi-biotinylate linker are bound tothe same streptavidin tetramer. In certain preferred embodiments of thepresent invention, the bis-biotinylated reactant of the invention is notmerely a linker comprising two (or more) biotins, but is instead amolecule that has a specific interaction/reaction with another componentin a reaction mixture. In further preferred embodiments of the instantinvention, all the biotins on a multi-biotinylated reactant bind to thesame biotin-binding agent, e.g., molecular complex such as astreptavidin dimer or tetramer. As such, a preferred complex comprisinga multi-biotinylated reactant of the invention further comprises only asingle biotin-binding agent.

In certain preferred embodiments, a reactant is modified to add twobiotinylation peptides, and two biotin molecules are subsequently boundto the biotinylation peptides (e.g., using a biotin ligase enzyme) toprovide a bis-biotin tag on the reactant. Where the reactant of interestis a protein, multiple, preferably tandem sequences encodingbiotinylation peptides are cloned into a DNA sequence encoding theprotein of interest such that expression results in a fusion proteincomprising the protein of interest linked to the multiple biotinylationpeptides, which are subsequently biotinylated. In preferred embodiments,the two biotinylation peptides occur within a single “biotinylationregion,” e.g., at one end of the reactant of interest, preferablytandemly arranged. For example, with a protein of interest, abiotinylation region is preferably at the C-terminal or N-terminal endof the protein. In alternative embodiments, two separate biotinylationregions can be engineered into a reactant of interest, where eachcomprises a single biotinylation peptide. For example, one could be atthe C-terminus of a protein, while the other is at the N-terminus. Thelocation of biotinylation regions within a reactant of interest is notlimited to the ends, and can occur internal to the reactant, as well.However, where it is required that the reactant maintain a givenactivity, the location of the biotinylation peptides, and eventuallocation of the biotin moieties, cannot interfere with this activity. Itis well within the skills of the ordinary artisan to determine whichportions of a given reactant are necessary for its activity, and whichportions are amenable to such modification.

Preferably the biotinylation occurs in vivo, which provides biotin tagsthat can be used to purify the fusion protein from a cell extract. Inother embodiments, it can be carried out in vitro at some point duringthe lysis and purification process. Following biotinylation andisolation of the biotin-tagged protein, the two biotin molecules(bis-biotin moiety) that are now bound to the biotinylation peptides canbe further bound to two adjacent sites (e.g., on the same dimer) on astreptavidin tetramer. Introduction of streptavidin results in assemblyof a protein-biotin-streptavidin complex that has two open binding siteson the streptavidin tetramer, which can be bound to biotins linked toanother reactant having at least two biotin tags, or bound to two otherbiotinylated reactants. Alternatively, the streptavidin introduced mayalready be bound to another molecule, e.g., a mono-biotin orbis-biotin-tagged reactant. In certain preferred embodiments, thestreptavidin is already bound to a single, bis-biotin-tagged label(e.g., fluorescent dye).

Particularly preferred compositions of the invention comprise a singlestreptavidin molecule having all four binding sites occupied, but boundto only two reactants in a 1:1 stoichiometry, e.g., where each of thetwo reactants is linked to the streptavidin molecule via two biotintags. For example, binding of a bis-biotin-tagged protein to abis-biotin-labeled streptavidin (streptavidin bound to a label (e.g.,fluorescent dye molecule) having a bis-biotin tag) results in a complexhaving a 1:1 stoichiometry with respect to the two bound molecules,i.e., the protein and the label, since only one protein and one labelare bound to the streptavidin tetramer. The linkage between the proteinof interest and the label, via the streptavidin tetramer, can besubsequently used to identify or otherwise detect the protein duringfurther analysis. Although a label is bound to the streptavidin in thisexample, the streptavidin can be bound to any molecule that one wishesto link to the protein of interest, e.g., another protein, a nucleicacid or nucleotide, a small molecule or drug, gold or other metallicparticle, antibody or antigen, affinity tag, RFID tag, barcode (e.g.,nucleic acid or polypeptide barcode), or a different type of label(e.g., mass label, spin label, etc.). Further, the streptavidin canalternatively be linked to a surface, e.g., through a bis-biotinlinkage, e.g., for purification or other manipulation of the protein.Surfaces contemplated include, but are not limited to, beads (e.g.,magnetic beads), columns (e.g., for chromatography), microarrays,semi-solid surfaces, waveguide substrates, within nanoholes (e.g., atthe bottom of zero-mode waveguides) on an array, etc.

A bis-biotin tag can be arranged in a linear or branched orientation,depending on the structure of the reagent to be tagged. A linearorientation is preferred where the reactant is a fusion protein havingbiotinylation peptides oriented in tandem, with or without spacers inbetween them, at one end of the fusion protein. Such a fusion proteincan be expressed in vivo where biotinylation sequences are added to thegene for a peptide of interest, similar to the method of adding a singlebiotinylation peptide to a protein of interest described above. Abranched orientation can be provided using conventional biochemicalmethods, e.g., by biochemically synthesizing a branched linker havingtwo bintinylation peptides, each on a separate branch. This syntheticlinker is bound to a reactant of interest and, preferably, subsequentlybiotinylated to provide a branched bis-biotin tag.

Streptavidin is a dimer of dimers. There is a distance of about 19-20Angstroms between the carboxyl moieties of biotins bound to the twobinding sites on one of the two dimers, i.e., “adjacent biotins.”(Similar distances are also found for tamavidin and avidin.) As such, adistance or “linker length” between the two biotins of a bis-biotinmoiety of about 19-20 Angstroms or greater is able to accommodatebinding of both biotins to binding sites on a streptavidin dimer. Since,fully extended, the 15 amino acids of the biotinylation peptides canspan over 50 Angstroms, tandemly repeated biotinylation peptides in afusion protein provide more than enough of a distance between thesubsequently bound biotin moieties to allow binding to adjacent bindingsites on one of the two streptavidin dimers, as long as the secondaryand/or tertiary structure of the polypeptide region between the boundbiotin moieties does not shorten the actual distance between them toless than 19-20 Angstroms. Where the linker length is too short to allowbinding of both biotins, the construct would favor daisy-chaining ofstreptavidin tetramers, where one biotin of the bis-biotin would bind toone streptavidin complex and the other biotin would bind to a secondstreptavidin complex, thereby linking the two streptavidin complexestogether. As such, in preferred embodiments the biotinylation region ofa reactant provides a distance between bound biotin moieties of at least20 Angstroms, more preferably at least 25, 30, 35, 40, 45, 50, or 60Angstroms. Likewise, where the biotins in the bis-biotin tag are too farapart, daisy-chaining of streptavidin molecules once again becomesfavored over binding of both biotins to the same streptavidin dimer.More information on daisy-chaining of streptavidin can be found inRingler and Schulz (2003) Science 302, 106-109, incorporated herein byreference in its entirety for all purposes. As such, in preferredembodiments, the linker length is about 20-70 angstroms, more preferablyabout 20-60 angstroms. Given a flexible linking portion of the reactantof interest, the linker length can also change as the linking portionbends and flexes, as will be understood by those of skill in the art.Further, secondary and tertiary structure of a polypeptide linker willchange the actual distance between two biotin moieties, so the distancesprovided here refer to the distance that is spanned in order to bindboth biotin moieties to desired binding sites, e.g., on a streptavidincomplex, and are not necessarily “stretched out” lengths of a linker,e.g., based upon its primary structure.

In other embodiments, a single reactant can be tagged with threebiotins, i.e., a “tris-biotin” tag. The tris-biotin-tagged molecule isbound to a streptavidin molecule, leaving a single binding site open fora single mono-biotin-tagged molecule. Similar to thetwo-bis-biotin-tagged strategy, this strategy also provides for a 1:1stoichiometry of molecules bound to a single streptavidin molecule.However, the spacing between the bound biotins must be able toaccommodate the span from one side of the streptavidin molecule, wheretwo binding sites are occupied, to the other side where the third sitewill be occupied. The distance between biotin-binding sites on differentdimers of the streptavidin complex is 29.6 Angstroms, and that distancegoes through the center of the tetramer complex rather than wrappingaround the outside as would be required for a tris-biotin complex. Inorder for a tris-biotin tag to occupy both biotin-binding sites on onedimer and reach to the other side for a biotin-binding site on the otherdimer, the linker would need to accommodate a distance of about 70Angstroms, and would need to be flexible enough to allow the curvaturerequired to wrap around the complex. One disadvantage to using atris-biotin tag is that it's more likely to bind to two streptavidinmolecules rather than three binding sites on a single tetramer, whichcan cause the daisy-chaining of streptavidin molecules, but thelikelihood of this occurring is dependent on the concentration ofstreptavidin and the tris-biotinylated reactant.

The inventors have recognized the value of using multi-biotinylatedreagents to effectively change the valence of a tetravalent bindingpartner (e.g., streptavidin, traptavidin, avidin, NeutrAvidin, etc.)such that it functions as a divalent binding partner by linking multiplebiotin moieties to a single reactant such that multiple binding sitesare blocked on the tetravalent binding partner when the reactant isbound. For example, binding these reagents to streptavidin moleculeseffectively reduces the number of unoccupied binding sites on thetetramer to facilitate the construction of homo- or hetero-dimers ofbiotinylated reactants. In preferred embodiments, binding of abis-biotinylated reagent to streptavidin blocks two binding sites on thetetramer while two binding sites remain unoccupied. Thisbis-biotinylated streptavidin tetramer can subsequently be used toconstruct a complex having a 1:1 stoichiometry for reactants bound tothe streptavidin tetramer by introducing a second reactant that is alsobis-biotinylated. A variety of schemes are possible, and certainpreferred embodiments are illustrated in FIGS. 1-7. Other uses ofbis-biotin binding reagents are described in Wilbur, et al. (1997,Bioconjug. Chem. 8(6):819-832) and International Patent Publication No.WO 1999/060400, both of which are incorporated herein by reference intheir entireties for all purposes.

In a simple embodiment, a bis-biotinylated reactant is a non-reactivecomponent that serves to block two of the sites on a tetrameric complex.This results in a tetrameric complex having only two binding sitesavailable for further binding as illustrated in FIG. 1. The tetramericcomplex bound to the bis-biotinylated reactant can be subsequently usedas a divalent binding partner to link together two mono-biotinylatedreactants in a 1:1 stoichiometry, which can be the same reactant toproduce a homodimer, or different reactants to produce a heterodimer. Inthe latter case, mixtures of products can be obtained (e.g., comprisingboth homo- and hetero-dimers) and subsequent purification steps areperformed to isolate the desired combination, FIG. 1 illustrates abranched, bis-biotin moiety linked to a non-reactive component, which isexposed to a tetrameric streptavidin to produce a complex having onlytwo open biotin-binding sites. Two mono-biotinylated reactants (Reactant1 and Reactant 2) are introduced, either simultaneously or serially, andeach binds to one of the open biotin-binding sites. Reactant 1 and 2 canbe different reactants, or can be identical reactants, as noted above.This method is especially beneficial when it is desirable to colocalizeReactant 1 and Reactant 2, e.g., to increase the kinetics of a reactionbetween them. For example, colocalization of two components of abiochemical reaction will promote the reaction by increasing thelikelihood the two components will interact with one another, e.g., anenzyme is likely to react more quickly with a colocalized enzymesubstrate that an enzyme substrate free in solution. Similarly, where itis desirable to link two reactants together, colocalizing them willfacilitate the linkage by increasing their local concentration withrespect to each other. Yet further, colocalizing reactants that act inconcert, e.g., in a metabolic pathway or as a cofactor/enzyme pair, isbeneficial since the colocalization increases the efficiency of theircooperative functions. (These benefits of colocalization apply equallywell to other specific embodiments described herein, such as those inwhich two bis-biotinylated reactants are bound to the same streptavidinmolecule, as further described below.) As noted elsewhere herein, otherbinding partners can also be used in the compositions and methodsdescribed herein. For example, the bis-biotin moiety in FIG. 1 could bereplaced with two strep-tag peptides and the streptavidin could bereplaced with a streptactin molecule, e.g., as described in U.S. Pat.No. 7,981,632.

In another embodiment, a non-reactive component can be a detectablelabel (e.g., fluorescent dye) is bis-biotinylated and bound to atetravalent streptavidin to produce a labeling reagent as illustrated inFIG. 2. A bis-biotinylated reactant of interest is combined with thislabeling reagent to produce a complex wherein the reactant of interestis linked to the detectable label in a 1:1 stoichiometry. This strategycan be used to differentially label any number of different reactants byexposing them to labeling reagents having different detectable labels.The labeled reactants can be subjected to further analysis that uses thelabels, e.g., to track or quantitate the reactant in an experimentalsystem. Although a fluorescent dye is provided as an exemplarydetectable label, other detectable labels can also be used in thisapplication, e.g., mass labels, spin labels, quantum dots, metallicparticles, and others known in the art and/or described elsewhereherein.

In related embodiments, other bis-biotinylated moieties can be linked toreactants of interest through binding to a tetravalent complex. Forexample, rather than a detectable label the streptavidin can be bound toa nucleic acid barcode, polypeptide barcode, or RFID tag to form anidentification tag, which is then linked to a reactant of interest. Inanother application, an affinity or “purification” tag isbis-biotinylated and bound to a streptavidin to be used as an affinityreagent useful for capturing biotinylated reactants of interest bound tothe streptavidin. In certain preferred embodiments, an affinity tag is amagnetic bead that is immobilized proximal to a magnet or an antibodythat binds to an antigen on a surface. Immobilization of the affinitytag, e.g., to a magnet or antigen-coated surface, respectively, allowremoval of components of a mixture that are not bound to thestreptavidin, i.e., that are not the reactant of interest. Other typesof purification tags include, but are not limited to, FLAG tags,reactive moieties (e.g., thiol or SNAP tag labels). In furtherembodiments, such labeling reagents (or affinity tags or identificationtags) comprising two available binding sites are used for dual purposes,e.g., to both colocalize two mono-biotinylated reactants and label thatcolocalized pair. For example, with reference to FIG. 1, thenon-reactive component could be a label (or other tag), in which casethe two reactants would not only be colocalized, but also linked to thelabel or tag, e.g., for tracking, quantitation, isolation,identification, etc. In yet further embodiments, the non-reactivecomponent could be an immobilization tag, e.g., an agent that bindsdirectly or indirectly to a solid surface. In such embodiments, thereactant or reactants of interest can be bound to the complex eitherprior or subsequent to immobilization of the tetrameric complex.

In another aspect of the invention, colocalization of two reactants isprovided by providing bis-biotin tags on both reactants and bindingboth, either simultaneously or sequentially, to the tetravalent complex.An exemplary illustration is provided in FIG. 3, where Reactant 1 isbound to both binding sites of one of the streptavidin dimers, andReactant 2 is bound to the two binding sites on the other dimer. Thisfigure depicts Reactant 1 with a branched biotinylation tag, andReactant 2 with a linear biotinylation tag, but the method is alsooperable with both having linear tags, or both having branched tags.Where direct interaction between the reactants is an object of thecomplex, the length of the linkers connecting the reactants to theircomponent tags is designed to provide sufficient movement to allow thatinteraction. For example, where one reactant is a cofactor or substrateand the other is an enzyme, the linkers are sufficiently long to allowproductive interaction between the reactants, e.g., to promote enzymeactivity. Similarly, where the reactants are to be directly joinedtogether, e.g., for attachment of a tag (reactant 1) to a molecule ofinterest (reactant 2), the linkers are sufficiently long to allow thereactants to orient with one another in a configuration that promotesthe joining. Since the two reactants use all four binding sites, abiotin- or bis-biotin-tagged label cannot also be bound to thebiotin-binding sites on the dimers of the streptavidin, but a label orother tag can be linked to other sites in the complex (e.g., otherregions of the streptavidin tetramer) by methods known and routine inthe art.

FIG. 4 provides an illustrative example of another method for using thetetravalent complex to link two reactants together with a 1:1stoichiometry wherein one reactant is tris-biotinylated and the otherreactant is mono-biotinylated. Since there are only four binding siteson the streptavidin tetramer, only one of each type of biotinylatedreagent can be bound to a single tetramer. Which reagent has thetris-biotin tag and which has the mono-biotin tag depends on the needsof the practitioner and the requirements for strong and stable bindingof each. For example, where a subsequent reaction takes place in thepresence of one of the reagents, that reagent can be chosen to be themono-biotin-tagged reagent so that upon dissociation during the reactionanother molecule of the reagent is readily available to bind to the openbinding site. In preferred embodiments, the tris-biotinylated reagent isbound to the streptavidin first. This order ensures that only a singleone of the mono-biotinylated reagents binds because only a singlebinding site is available after binding of the tris-biotinylatedreagent. As in the above-described embodiments, the reactants can be anyreactants that are amenable to such biotinylation, e.g., nucleic acids,proteins, drugs, carbohydrates, cofactors, detectable labels, affinitytags, identification tags, immobilization agents, and the like.

Highly negatively or positively charged proteins (also termed“supercharged” proteins; see, e.g., Thompson, et al. (2012, MethodsEnzymol. 503: 293-319, incorporated herein by reference in its entiretyfor all purposes) have superior properties in folding, lack ofaggregation, and the being taken up by cells (in the case of thepositively charged ones). In certain aspects, the present inventionprovides “supercharged” macromolecular complexes that have many usefulproperties similar to those of supercharged proteins. In certainpreferred embodiments, a highly charged moiety is bis-biotinylated andbound to a streptavidin tetramer to leave two open binding sites. Areactant of interest, e.g., a protein, nucleic acid, small molecule,label, or any other reagent that the practitioner wishes to link to thehighly charged moiety, is also bis-biotinylated and bound to the twoopen binding sites. This configuration provides a 1:1 stoichiometrybetween the highly charged moiety and the reactant of interest. Inalternative embodiments, the number of biotins on the highly chargedmoiety and/or the reactant can be varied. Alternatively or in addition,multiple, mono-biotinylated reactants and/or highly charged moieties canbe bound to the complex. For example, the highly charged moiety can bebis-biotinylated while two bound reactants each have only a singlebiotin tag, or vice versa. In certain preferred embodiments, the highlycharged moiety is a highly negatively charged moiety, such as apolyphosphate chain. For example, highly negatively chargedpolyphosphate groups are very stable given a bis-biotin tag linked tostreptavidin.

As noted above, although described primarily in terms of a streptavidintetramer bound to biotinylated reagents, it will be clear to theordinary practitioner that streptavidin can be replaced with tamavidin,NeutrAvidin, and other multivalent molecules mentioned herein and knownin the art that have a high affinity for biotin. See, e.g., Takakura, etal. (2009) FEBS Journal 276:1383-1397, incorporated herein by referencein its entirety for all purposes. Alternatively, other high-affinitybinding partners (e.g., streptactin and the strep-tag peptides) can beused in the place of the streptavidin-biotin combination. Further, wherethe complex is intended to link a detectable label to a singlebiotinylated reactant, the biotinylated reactant could comprise fourbiotin tags that occupy all four binding sites of the streptavidin (orother multivalent biotin-binding partner) where the label is linked tothe streptavidin at a different location, e.g., through surface lysinessuch that the linkage does not interfere with the binding of the singletetra-biotinylated reactant.

The methods and compositions provided herein are also useful inidentification and quantification of a protein of interest in a complexmixture. As described above, a protein of interest is first cloned withtandem sequences encoding biotinylation peptides. The cells containingthe sequences encoding the protein and biotinylation peptides are grownand lysed. The lysate is exposed to biotin and a biotinylation enzyme toadd biotin moieties at the biotinylation peptides, and subsequentlyincubated with a complex comprising a streptavidin linked to adetectable label. The detectable label can be mono-biotinylated andbound to one biotin-binding site on the streptavidin tetramer, or can belinked to the streptavidin in a manner that does not block any of thebiotin-binding sites (e.g., “body-labeled”). FIG. 5 provides anillustrative example of the method, showing how a bis-biotinylatedprotein of interest (Protein 1) binds to a streptavidin bound to abody-linked label (i.e., linked to a portion of the streptavidintetramer that is not a biotin-binding site) while non-specific proteinsremain unbound (Proteins 2, 3, and 4). The lysate is then incubated for20 minutes at 90° C. in the presence of SDS (sodium dodecyl sulfate) orother appropriate detergent, and subsequently subjected toelectrophoresis. Only the streptavidin tetramers that have tandembiotins bound (i.e., a bis-biotin bound to both biotin-binding sites onone of the streptavidin dimers in the tetramer) remain tetrameric. Thosestreptavidin tetramers with no bis-biotin bound fall apart, mostly intomonomers, by the harsh treatment. Although there is some literature onthermal stabilization of streptavidin by biotin, this finding is asurprising result, since the ordinary artisan would not have expectedthat binding of one bis-biotin tag to one dimer of a streptavidintetramer to stabilize the entire tetramer under such extreme conditions.For example, Holmberg, et al. reported that biotin-streptavidininteractions can be disrupted in a nonionic aqueous solution at atemperature above 70° C. (Electrophoresis 2005, 26:501-510), and Xia, etal. showed experiments in which about half of streptavidin tetramers ina solution unfolded after only about 9±1 to 11±2 minutes at 70° C.,depending on the method of calculation (Biochemistry (2012) 51:100-107),both of which are incorporated herein by reference in their entiretiesfor all purposes. It was unexpected that a single bis-biotinylatedreactant could stabilize a streptavidin tetramer in the presence of SDS,for 20 minutes at 90° C., and specific details of the experimentsrevealing this unexpected result are provided in the Examples herein.The concentration of the remaining streptavidin tetramers isproportional to the amount of the protein of interest in the lysate andcan be quantitated through standard scanning techniques that detect theamount of label present in the band corresponding to the tetramericstreptavidin. That is, the amount of label present is proportional tothe amount of tetramer present, which is proportional to the amount ofthe protein of interest present in the lysate. The label present in theother band(s) on the gel represents the label bound to streptavidin thatfell apart during the high-heat incubation in SDS. Optionally, to ensurea 1:1 stoichiometry between the body-labeled tetramer and thebis-biotinylated protein (which could bind to both dimers), one or twobiotin binding sites on one of the streptavidin dimers can be blocked,e.g. using a mono-biotinylated non-reactive component, prior to exposureto the cell lysate. Alternatively, during gel analysis the complexeshaving two proteins bound will migrate in a separate band, and theamount of protein in the slower-migrating band will be computed toaccount for two proteins for each label. In embodiments using amono-biotinylated label, the label itself can serve to block binding ofthe bis-biotinylated protein to one of the two dimers, leaving the otherdimer available for binding. Optionally, a non-reactive,mono-biotinylated component can be bound to the second binding site ofthe dimer to which the label is bound. More preferably, purificationmethods, e.g., mass-based methods, are used to ensure that the labeledstreptavidin has only a single mono-biotinylated label bound prior tobinding the protein of interest. Yet further, where the existence of twolabels detectably changes the migration of the complex, the extrapurification step is unnecessary since the amount of protein of interestin the band corresponding to the double-labeled complex is analyzed totake into account that a single protein corresponds to two labels inthat band.

In alternative embodiments, the detectable label bound to thestreptavidin is bound at two binding sites via a bis-biotin tag. Thismode provides a cleaner 1:1 stoichiometry between the protein ofinterest and the dye, which improves the calculation of the amount ofthe protein that is present in the tetramer band because theavailability of only two binding sites for the protein of interestensures that only a single one will bind to the streptavidin tetramer.This strategy requires a slightly more complex gel separation step sincethe bis-biotinylated label will hold the tetramer together during ahigh-heat detergent incubation whether or not the protein of interest isbound. An embodiment of an appropriate gel separation strategy isillustrated in FIG. 6, which shows the two streptavidin tetramercomplexes: one with only the bis-biotinylated dye bound, and the otherwith both the bis-biotinylated dye and the bis-biotinylated protein ofinterest (Protein 1) bound. A non-specific “contaminating” protein(Protein 2) is also shown. Following electrophoresis, the gel will showtwo bands that correspond to these two dye-labeled complexes. If thecomplex comprising the protein of interest migrates at a distinctlydifferent position on the gel, the practitioner can readily distinguishwhich band should be analyzed to measure the quantity of this protein.However, if the two complexes migrate together or very close to oneanother, an additional binding step can be performed prior to gelelectrophoresis to better separate the migration of the two complexes.In certain preferred embodiments, a third bis-biotinylated non-reactivecomponent (NRC) is added to the mixture. Since only the complex lackingthe protein of interest has any binding sites available, this thirdbis-biotinylated NRC will only bind to that complex. The NRC causes thecomplex lacking Protein 1 to migrate significantly differently than thecomplex comprising Protein 1, e.g., slower or faster. As a result, theelectrophoresis will provide separation of the two complexes, and thecomplex comprising the protein of interest can be quantified todetermine its quantity in the mixture. In alternative embodiments,rather than radically changing the migration of the complex lacking theprotein of interest, the NRC can also be a quenching moiety thatquenches the signal from the label, rendering the complexes lacking theprotein of interest “invisible” to the subsequent detection andanalysis. Quenching molecules are well known and readily accessible inthe field to which the invention pertains.

In addition to the stoichiometry advantage, another benefit to usingmulti-biotin-tagged molecules is that the binding to streptavidin istighter and more stable than that of mono-biotin-tagged molecules, i.e.,more than two-fold greater stability. As such, where a high stabilitybinding of two reactants to streptavidin is desired, usingbis-biotin-tagged molecules is preferred. Alternatively, where increasedstability is more important for a first one of the molecules and asingle-biotin-based stability is sufficient for the second, using thetris-biotin tag (as described elsewhere herein) on the first moleculeand a mono-biotin-tag on the second is preferred. Without wishing to bebound by theory, one likely reason for the increased stability is theavidity of the binding of a bis-biotin tag to a streptavidin tetramer.In proteins, avidity is the combined strength of multiple bondinteractions. Avidity is the combined synergistic strength of bondaffinities rather than the sum of bonds. As such, the dissociation of asingle biotin moiety from a biotin-binding site on the streptavidin israpidly followed by reassociation due to close proximity of the releasedbiotin, which is effectively tethered to the streptavidin molecule bythe biotin moiety that is still bound. As such, most of the time atleast one biotin is bound, and if one is not bound it is very near andlikely to rebind quickly. As long as both biotins don't dissociatesimultaneously, the binding of the bis-biotin to the streptavidin ismaintained.

In certain aspects, methods are provided for creating preparationscomprising primarily streptavidin with only a single bis-biotinylatedreactant bound and having two free biotin-binding sites. In preferredembodiments, separation of streptavidin complexes comprising a singlebis-biotinylated reactant from complexes comprising two bis-biotinylatedreactants is accomplished using ion-exchange column purificationmethods. For example, where the bis-biotinylated reactant is anegatively charged dye molecule, the charge on the dye facilitatespreparation on the ion exchange column since complexes having two dyesbound will have a significantly more negative charge associated withthem. A linear gradient of an acetonitrile-containing buffer is used toelute the complexes, and the fractions containing the streptavidingcomplex comprising a single bis-biotinylated reactant are pooled andconcentrated. A detailed protocol is provided herein in the Examplessection. The fractions that do not contain the desired complex can besaved and reused in future preparations, either directly (as in the caseof the streptavidin complexes having no bis-biotinylated reactantsbound) or after stripping off any remaining bis-biotinylated reactants.

In another aspect of the invention, kits are provided for labelingreactants using a tetrameric complex comprising a bis-biotinylatedlabel. This invention also embraces kits which are useful for linkingtwo individual reactants, which may be identical or different, via atetrameric complex at a desired stoichiometry, preferably 1:1. Incertain embodiments, such kits comprise streptavidin (or othertetrameric, biotin-binding complex) and a bis-biotinylated label, suchas a mass label, spin label, or fluorescent dye. Alternatively, suchkits comprise a bis-biotinylated label already bound to the tetramericcomplex. Other constituents of the kits may comprise host cells suitablefor cloning a biotinylation sequence into the gene of a protein ofinterest, and, preferably obtaining expression from the protein ofinterest; and a tetrameric complex coupled to a solid support; abiotinylation enzyme such as purified BirA. Instructions are alsooptionally included for various aspects of the methods, e.g.,instructions for analysis and purification of the proteins expressedusing these kits, purification of tetrameric complexes comprising asingle, bis-biotinylated label, and analysis of quantities of proteinsof interest in a cell lysate. Preferably, the host cells will express abiotinylating enzyme. Optionally, polynucleotides which, whentransformed into host cells, cause the production or overproduction ofbiotinylating enzymes may be supplied in the kits, or the host cellsprovided with the kits may be already modified to produce orover-produce biotinylating enzymes. However, for some applications theabsence of biotinylating enzyme in the host cell may be advantageous.For example, the kit user may prefer to biotinylate the expressed fusionproteins in vitro.

III. Applications

Various applications of the methods and compositions have been describedin the embodiments set forth above. For example, the tetramericcomplexes comprising a bis-biotinylated label (e.g., fluorescent dye)are very effective labeling reagents for bis-biotinylated reactants ofinterest. The methods teach how to purify the label-tetramer complexesfrom doubly-labeled complexes. The purified complexes efficiently bindto the bis-biotinylated reactant of interest, and the resulting complexeffectively links the label to the reactant in a highly stable complex.

Also described at length above, colocalization of two reactants (two ofthe same reactant or two different reactants) is also a highlybeneficial application of the invention. The compositions providedherein can provide colocalization of different proteins, such as enzymesthat work cooperatively. This can function to provide “pseudo-fusionproteins” that behave similar to traditional fusion proteins, but whichcan be assembled much more quickly without the need to clone twoproteins together. Examples of such enzyme include, but are not limitedto, polymerases and nucleic-acid-modifying enzyme (e.g., repair enzymes,topoisomerases, methyltransferases, etc.). Other reactants that arebeneficially colocalized are those that participate in the samemetabolic pathway, e.g., synthetic biochemical pathways. Yet further,some reactions benefit by having higher local concentrations ofcomponents having protective functions, e.g., those that reduce damageto reaction components under excitation illumination. In otherembodiments, reactants are colocalized to enhance reaction kineticsbetween them, e.g., enzymes acting on enzyme substrates, and this canprovide a consolidation and/or acceleration of an enzymatic pathway.Binding interactions also benefit by colocalization of binding partners,e.g., antibody-antigen pairs, receptor-ligand pairs, etc. The methodsand compositions herein can also be used to enhance the activity ofstimuli-responsive polymers used to gate biomolecular reactions byensuring their colocalization with the active site of proteins withwhich they interact, e.g., as described in Shimoboji, et al. (2001)Bioconjugate Chem. 12:314-319, which is incorporated herein by referencein its entirety for all purposes.

The compositions can also be used to enrich a nucleic acid mixture forspecific sequences of interest by using a bis-biotinylatedoligonucleotide (e.g., a probe or primer) to “fish” for the specificsequences in the mixture. The oligonucleotide is designed to becomplementary to the sequence or sequences of interest in a nucleic acidmixture. Preferably, the nucleic acid mixture is fragmented prior toexposure to the bis-biotinylated oligonucleotide. In especiallypreferred embodiments, the fragmentation is specific to ensure that acontiguous sequence in the desired nucleic acid is complementary to theoligonucleotide. In some embodiments, the fragmentation provides a 3′end that is complementary to a portion of the oligonucleotide near or atthe 5′ end. After exposing the fragmented nucleic acid mixture to thebis-biotinylated oligonucleotide under conditions that promoteannealing, a polymerase enzyme is used to extend the oligonucleotide,thereby strengthening the interaction between the oligonucleotide (nowextended) and the sample nucleic acid of interest. Immobilization of theextended oligonucleotide/sample nucleic acid allows the other nucleicacids in the mixture to be removed, thereby isolating the sequence(s) ofinterest and providing mixture enriched for those sequences. Followingremoval of the non-specific sequences, the remaining nucleic acids canbe further analyzed. For example, the duplex between the extendedoligonucleotide and sample nucleic acid can be removed from thebis-biotin moiety and subjected to a sequence reaction, amplified,and/or cloned. Alternatively, only one of the extended oligonucleotideor the selected sample nucleic acid is subjected to further analysis,e.g., single-strand sequencing, amplification, etc. In relatedembodiments, other types of affinity pairs can be used. For example, incertain embodiments, the oligonucleotide comprises twostreptavidin-binding aptamers rather than a bis-biotin moiety, e.g., asdescribed elsewhere herein. Like the bis-biotin moiety, the two aptamersare used to immobilize and isolate the sample nucleic acid of interest,optionally after extension of the oligonucleotide.

In certain aspects, the invention provides methods for detectingprotein-protein interactions between two biotinylated (preferablybis-biotinylated) proteins using streptavidin molecules having nucleicacid tags or “barcodes.” In a preferred embodiment, a firstbis-biotinylated protein is bound to a first tag-labeled streptavidinmolecule, and a second bis-biotinylated protein is bound to a secondtag-labeled streptavidin molecule. The two proteins, now linked to thetagged streptavidin molecules, are combined in a reaction mixture thatpromotes an interaction between them, e.g., covalent or noncovalentbinding, catalytic interactions, or other interaction that causes theirpermanent or transient colocalization. The reaction mixture alsocomprises a ligase and promotes ligation of the free ends of the twotags when the proteins are bound to the streptavidin. An illustrativeembodiment is provided in FIG. 7, in which Protein 1 and Protein 2 areeach bound via a bis-biotin linkage to a different streptavidin. Thestreptavidin bound to Protein 1 comprises a nucleic acid tag, Tag 1; andthe streptavidin bound to Protein 2 comprises a nucleic acid tag, Tag 2.Interaction of these proteins causes localization of the tags, which areligated together at the ends. Subsequent cleavage of the tags atcleavage sites (each indicated by an asterisk) releases them from thebis-biotin tags, and the ligated tags can be further manipulated, e.g.,by amplification, circularization, sequencing, gel-based analysis, etc.

Detection of a ligation event serves as a proxy for the interactionbetween the two proteins. For example, where each of the tags has adifferent primer binding site at an end distal to the end of the tag atwhich ligation occurs, the tags, ligated together, are a template forexponential amplification, e.g., by PCR; tags that are not ligatedcannot be exponentially amplified since they have only one primer site.The product of amplification can be detected by gel-based methods, orcan be subjected to a nucleic acid sequencing reaction. Determining theactual sequence rather than just the size of the amplification productis preferred since it allows the practitioner to combine multipledifferent proteins with multiple different tags, and the sequence of theamplified product is used to identify which of the multiple proteinsbound to each other. In some embodiments, the nucleic acid tags aresingle-stranded and the ligation is facilitated by using a “splint”oligo complementary to the ends of the tags, where binding of the oligoto the tags brings the ends of the tags into position for efficientligation. In other embodiments, the nucleic acid tags aredouble-stranded and the ligation is facilitated by complementaryoverhangs of the tags. In certain embodiments, the ligated tags arereleased from the proteins, e.g., by endonuclease digestion, andcircularized prior to further analysis. For a single-stranded constructformed by ligating two single-stranded tags, the circularization isaccomplished in various ways, e.g., by ligation of the cut ends, e.g.,using a splint oligo as described above; or by synthesizing acomplementary strand and attaching stem-loop adaptors to thedouble-stranded ends produced. Similarly, for double-stranded constructformed by ligating two double-stranded tags, the double-stranded terminiformed by the endonuclease reaction can be directly ligated together toform a double-stranded circular construct, or can be ligated tostem-loop adaptors to form a single-stranded circular construct. Thetags on different protein can also differ by more than their canonicalbase sequence. For example, in some embodiments the tags comprisemodified bases that can be subsequently detected during a sequencingreaction. Methods for detection of modified bases during sequencingreactions are known in the art and described at length in InternationalPatent Application Publication No. WO2012065043, incorporated herein byreference in its entirety for all purposes.

The bis-biotinylated compounds of the invention also find utility in themedical sciences by providing a very stable connection between astreptavidin and an agent of interest, where the agent is to be retainedin the kidney for a number of days, e.g., to treat a kidney disorder. Inthe body, streptavidin accumulates in the kidney and has been observedto remain in the kidneys of mice, rats, and rabbits for 3-4 days. Thisaccumulation can comprise 15-20% of a dose of injected streptavidin, andis far greater than any accumulation in other tissues tested. (See,e.g., Schechter, et al. (1995) Kidney International 47:1327-1335,incorporated herein by reference in its entirety for all purposes.) Assuch, streptavidin can be used to deliver agents specifically to thekidneys, and such agents can include drugs, chemotherapeutic agents,radioactive isotopes, and the like. In certain aspects, the presentinvention provides such ligands linked to streptavidin via a bis-biotinlinkage, which provides the benefit of better controlling the dosage ofthe agents being delivered to the kidney. Further, it provides a meansto ensure a 1:1 stoichiometry of two different agents to the kidneys bylinking one of each of the two agents to each streptavidin molecule tobe introduced, and the higher stability of the bis-biotin linkageensures that both agents remain bound as they are ferried to the kidneysby the streptavidin molecule.

Another application for the bis-biotinylated compounds of the inventioninvolves delivery of various agents to target locations within anorganism, e.g., detectable labels for imaging/theranostics, smallmolecule therapeutics, cytotoxic agents targeted to tumors, etc. Thesetypes of applications have been previously performed usingmono-biotinylated compounds, e.g., see U.S. Patent Publications20110014151 and 20130052130, which are incorporated by reference intheir entireties for all purposes. Use of the bis-biotin tags instead ofthe mono-biotin strategies previously used will increase the stabilityof these delivery agents, thereby improving various aspects of theseapplications, including increasing the total amount of the agent that isdelivered to the target location and decreasing the amount ofpotentially hazardous payload (e.g., cytotoxins) that is dissociatedfrom the complex in non-target locations.

The methods and compositions herein can also be used to explore cellularsignaling systems. For example, the signaling between two cellularcomponents can be studied on at single-molecular-complex level bylinking one of each to a streptavidin molecule, thereby bringing themtogether and promoting interaction between them. Similarly, interactionsbetween two cellular components that do not naturally interact can alsobe explored in this way. Further, streptavidin polymers can be used toco-localize even more cellular components, creating a signaling networkcomprising multiple different components on a single streptavidinscaffold at a single reaction site. Further, the spatial relationshipbetween these components can be tested by changing their location withinthe scaffold. Introduction of such compounds into a cell allows in vivotesting of the configuration on cell function, growth, division, death,and the like. This also provides an opportunity to engineer cells forspecific purposes where an introduced signaling pathway provides abenefit to the cell, or to an organism into which the cell is to beintroduced. Such engineered cells can be therapeutic cells, or can becells engineered for biotechnological purposes, e.g., fuel production,pollution cleanup, production of commercially valuable molecules (e.g.,drugs, antibodies, etc.) See, e.g., Wei, et al. (2012) Nature488:384-388; and Sattely, et al. (2008) Natural Product Reports,25:757-793, both of which are incorporated herein by reference in theirentireties for all purposes.

The methods and compositions herein can also be used to enrich a nucleicacid mixture for loci of interest. In certain preferred embodiments, anoligonucleotide comprising a bis-biotin tag is complementary to anucleotide sequence within a locus of interest. Specific hybridizationof the oligonucleotide to the loci of interest and immobilization of theoligonucleotide via the bis-biotin tag allows for removal of other lociin the nucleic acid mixture, thereby enriching the mixture for the lociof interest. Where the mixture comprises double-stranded fragments,e.g., genomic DNA fragments, the nucleic acids are typically denaturedprior to exposure to the bis-biotinylated oligo. Preferably, thelocation of the bis-biotin tag is selected to ensure the 3′ end of theoligonucleotide can serve as a primer after binding to the loci ofinterest. This allows extension of the primer prior to removal of thenon-specific nucleic acids, thereby providing a stronger linkage to theloci of interest. Another benefit is the production of a double-strandedmolecule that can be removed from the bis-biotin tag, e.g., byendonuclease digestion, and can be further analyzed. In certainembodiments, the ends of the double-stranded molecule are capped withadaptors, e.g., adaptors having primer binding sites and/or stem-loopadaptors, to allow amplification and/or sequencing of the molecule. Thebis-biotin tag can be immobilized to any solid surface comprising abiotin-binding agent, e.g., streptavidin and others noted herein, andsuch a surface includes beads, arrays, columns, and the like.

The bis-biotin tags described herein can be used to improve assembly oftwo-dimensional ordered arrays of streptavidin crystals on a surfacedescribed by Ringler and Schulz (2003) Science 302, 106-109. The use ofbis-biotinylated streptavidin would make such arrays more robust, e.g.,to heat, etc. Further, attaching to two points in the streptavidintetramer would provide better control over where the neighboringmolecule is placed by virtue of the two tethers linked to the biotins.Yet further advantages can be achieved by taking advantage of thealternate stoichiometries provided by the bis-biotin linkages.

The bio-biotin linkages are also applicable to thelanthanide-streptavidin labeling methods used for medical imagingapplications with metal chelation described in Aime, et al. (2006)Coordination Chemistry Reviews, 250 (11-12), 2006, 1562-1579, which isincorporated herein by reference in its entirety for all purposes. Theycan also be used to improve the methods of Howarth and Ting for imagingproteins in living cells by providing a bis-biotin linkage at the cellsurface which can bind to a dimer of streptavidin with a higherstability than the mono-biotin tags they describe. Further, where thestreptavidin is further conjugated to a bis-biotin-linked biophysicalprobe of interest (e.g., a fluorophore or quantum dot), a further aspectof the method is improved as compared to the single-biotin-labeledprobe. See, e.g., Nature Protocols (2008) 3(3):534-545, which isincorporated herein by reference in its entirety for all purposes.

Yet further, the bis-biotin linkages described herein are beneficial tothe methods described in Chivers, et al. (2010) Nat. Methods7(5):391-393, which is incorporated herein by reference in its entiretyfor all purposes. The authors of that paper identified a mutantstreptavidin, traptavidin, that shows ˜10-fold slower biotin off-rate,increased mechanical strength, and improved thermostability. Theyfurther demonstrate that the motor protein FtsK can strip proteins fromDNA, rapidly displacing streptavidin from biotinylated DNA; traptavidinresisted displacement and thus indicated the force generated by FtsKtranslocation. The higher stability of the bis-biotin linkages wouldfurther stabilize the binding of DNA (or other reactant) to traptavidin(and also streptavidin). For example, the bis-biotin linkages willincrease resistance to displacement by motor proteins traveling along abiotinylated DNA molecule.

In additional aspects, the bis-biotin linkages provided herein can beused in combination with the SpyTag/SpyCatcher system developed by theHowarth lab and described in the literature, e.g., in Zakeri, et al.(2012) “Peptide tag forming a rapid covalent bond to a protein, throughengineering a bacterial adhesin,” PNAS 109(12):E690-7; Schoene, et al.(2014) Angew. Chem. Int. Ed. 53: 1-5; Zhang, et al. (2013) J. Am. Chem.Soc. 135: 13988-13997; and Fierer, et al. (2014) Proc. Natl. Acad. Sci.USA E1176-E1181, each of which is incorporated herein by reference inits entirety for all purposes. Briefly, the bacteria Streptococcuspyogenes has a fibronectin-binding protein FbaB that contains a domainwith a spontaneous isopeptide bond between a lysine residue and anaspartate residue. The Howarth lab split this domain and used thefragments to engineer two peptides, “SpyTag” and “SpyCatcher.” Theseindividual peptides are still capable of efficiently forming a covalentamide bond, and were used to create an intermolecular bond between amaltose binding protein fusion comprising the SpyTag peptide and theSpyCatcher peptide.

In certain embodiments of the present invention, a reactant is coupledto multiple bis-biotin tags using the SpyTag/SpyCatcher system in anovel, multiplex strategy. The general mechanism is to couple multipleSpyTags to a single reactant, and then expose this reactant-(SpyTag)_(n)to SpyCatchers, each of which is coupled to a bis-biotin tag. In doingso, the reactant is provided multiple bis-biotin tags for binding, e.g.,to avidin or streptavidin. The streptavidin can be bound the bis-biotintags before or after formation of the covalent bond between the SpyTagsand the SpyCatchers. For example, in preferred embodiments, the reactantis a protein that is fused to multiple SpyTags. The protein can beenzymatic or non-enzymatic, and in certain preferred embodiments, is afusion protein comprising a polymerase enzyme and multiple SpyTags.Methods of engineering fusion proteins are conventional in the art andwell known to the ordinary practitioner, e.g., as provided in Horton, etal. (1989) Gene 77(1):61-8, which is incorporated herein by reference inits entirety for all purposes. Although the number of SpyTags fused tothe reactant is generally determined by the practitioner based upon theintended use for the construct, the number will typically range from2-10 SpyTags, preferably from 3-8 SpyTags, and in certain preferredembodiments, at least four SpyTags. For example, FIG. 10 provides anillustrative embodiment of the bis-biotin tagging strategy in which fourSpyTags are fused to a polymerase enzyme in order to provide an ultimatecomplex (following covalent amide bond formation between the SpyTags andbis-biotinylated SpyCatchers) having four bis-biotin tags.

The resulting reactant-(SpyTag)_(n)-(SpyCatcher+bis-biotin tag), complexis useful for various applications. For example, where each bis-biotintag in the complex is bound to a streptavidin tetramer, the complex canbe immobilized on a surface comprising moieties that can bind to theopen binding sites of the tetramer, e.g., biotin or bis-biotin moietieson a surface. As noted elsewhere herein, surfaces contemplated include,but are not limited to, beads, microarrays, columns, semi-solidsurfaces, waveguide substrates, within nanoholes (e.g., zero-modewaveguides), etc. In other embodiments, multiple streptavidin tetramersare bound to accessory proteins that are beneficial in close proximityto the reactant. For example, where the reactant is an enzyme, theaccessory proteins can serve to provide a substrate to the enzyme, orcan further process a product of the catalytic activity. In a specificembodiment, the reactant is a polymerase enzyme and the accessoryprotein is a single-stranded binding protein that helps to removesecondary structure from a single-stranded template ahead of thepolymerase. In alternative embodiments, the reactant is a polymeraseenzyme and the accessory protein is a helicase that that helps to unwinda double-stranded template ahead of the polymerase. The availability ofmultiple streptavidin for binding accessory proteins is especiallybeneficial in cases where the accessory proteins function as multimers,as in the case of single-stranded DNA binding proteins.

In yet further embodiments, the multiple streptavidin molecules providebinding sites for tags, e.g., affinity tags, detectable tags (e.g.,dyes), and the like. In particular, the Applicants provide methods forusing the SpyTag/SpyCatcher system for providing polyvalency of labelingwhile excluding crosslinking of target proteins. For example, whereaffinity tags are bound to the streptavidin molecules, e.g., preferablyvia a bis-biotin moiety, the complex can be more efficiently purified acomplex having only a single affinity tag. In other embodiments,multiple detectable tags can be associated with the complex via thestreptavidin molecules. For example, a bis-biotinylated fluorescent dyecan be bound to each of the streptavidin molecules. In some embodiments,the dyes are all the same dye, thereby increasing the total emissionfrom the complex upon illumination with the appropriate excitationwavelength. Alternatively, the dyes can be chosen such that energytransfer occurs between two or more of them, e.g., as in the case offluorescence resonance energy transfer (FRET). As such, one or more dyesin the complex may be the same dye, and one or more may be differentdyes. The complexes can be assembled in various ways. In someembodiments, a bis-biotinylated dye is bound to the streptavidin priorto the streptavidin being bound to a his-biotinylated SpyCatcherpeptide, and the resulting complex is subsequently bound to the proteinwith multiple SpyTags, as illustrated in FIG. 11. In other embodiments,the bis-biotinylated SpyCatcher peptide is first bound to theprotein-SpyTag fusion, and subsequent to covalent bond formation,streptavidin is bound to the bis-biotin. Another bis-biotinylated moiety(e.g., a tag) is bound to the streptavidin either before or after thestreptavidin is bound to the bis-biotinylated SpyCatcher peptide. Whilethis disclosure refers primarily to the SpyTag peptide, but proteinsrelated to SpyTag may also be used, and such proteins have beendisclosed in the literature. See, e.g., Takakura, et al. (2009) FEBSJournal 276(5):1383-97, which is incorporated herein by reference in itsentirety for all purposes.

Additional applications of the methods and compositions described hereininclude use in single-molecule imaging on surfaces coated withbiotin-binding agents, such as streptavidin, avidin, traptavidin, etc.Imaging of such single-molecule assays is described in Zareh, et al.(2011) Microscropy Research and Technique 74:682-687, which isincorporated herein by reference in its entirety for all purposes. Theuse of bis-biotinylated reactants increase the stability of the bindingto the coated surface, thereby facilitating detection of the reactantsin the solution.

In light of the teachings herein, the benefits of the described methodsand compositions will be clear to the ordinary artisan, both in theapplications described herein, as well as other applications in the art.For example, bis-biotin tags are also useful in the construction oftwo-dimensional streptavidin arrays wherein crystals of streptavidin arebound to biotinylated lipid monolayers at the air-water interface, e.g.,as described by Farah, et al. (2001) Langmuir 17:5731-5735, which isincorporated herein by reference in its entirety for all purposes. Theuse of bis-biotinylated lipid monolayers would allow additional controlof the formation of such two-dimentional protein arrays by limiting thenumber of covalent bonds linking the streptavidin to the lipidmonolayer. They also provide similar advantages in cell surface displayapplications, e.g., as described in Furukawa, et al. (2006) Biotechnol.Prog. 22:994-997, which is incorporated herein by reference in itsentirety for all purposes, by increasing the stability and longevity ofthe streptavidin complex on the cell surface.

Those of skill in the art recognize from the description above that thepresent invention provides many advantages and more application thanprior art methods for using bis-biotinylation tags in variousapplications. The high binding affinity of the bis-biotin interactionprovides advantages for labeling, localization, detection,immobilization, and purification methods, as well. As can be appreciatedfrom the disclosure above, the present invention has a wide variety ofapplications. Accordingly, it is to be understood that the abovedescription and the following examples are offered by way ofillustration, and are not intended to be restrictive or limiting.

It should be readily apparent to one skilled in the art that variousembodiments and modifications may be made to the invention disclosed inthis application, including but not limited to combinations of variousaspects of the invention, without departing from the scope and spirit ofthe invention. The scope of the invention should, therefore, bedetermined not with reference to the above description, but shouldinstead be determined with reference to the appended claims, along withthe full scope of equivalents to which such claims are entitled. Unlessotherwise clear from the context or expressly stated, any concentrationvalues provided herein are generally given in terms of admixture valuesor percentages without regard to any conversion that occurs upon orfollowing addition of the particular component of the mixture. Allpublications mentioned herein are cited for the purpose of describingand disclosing reagents, methodologies and concepts that may be used inconnection with the present invention. Nothing herein is to be construedas an admission that these references are prior art in relation to theinventions described herein. Throughout the disclosure various patents,patent applications and publications are referenced. Unless otherwiseindicated, each is incorporated by reference in its entirety for allpurposes.

IV. Examples

Purification

In certain aspects, a method is provided for purifying abis-biotinylated streptavidin (i.e., a streptavidin bound to a single,bis-biotinylated molecule such that two binding sites are occupied bythe bis-biotin and two binding sites are open) away from both doublybis-biotinylated streptavidin (i.e., bound to two bis-biotinylatedmolecules such that all four binding sites are occupied by thebis-biotins and no binding sites are open) and streptavidin having allbinding sites unoccupied. In certain preferred embodiments, ion-exchangechromatography provides a way to separate different complexes formed bymixing bis-biotinylated molecules with streptavidin. For example, themethod is particularly effective when separating streptavidin complexescomprising charged groups, e.g., negatively charged dye molecules.

A typical ion-exchange purification of a single bis-biotin dye moietybound to streptavidin (e.g., the labeling reagent illustrated in FIG. 2)was performed as follows. A 1 ml aliquot of recombinant streptavidin at10 mg/ml solution (10% glycerol, 50 mM KOAc, 5 mM Tris pH7.4) was thawedand placed in a 5 ml tube. The bis-biotin dye was added to 4 mls ofBuffer A (5 mM Tris HCl pH 7.4, 20% acetonitrile) to a finalconcentration of 18.75 μM. In 250 μl aliquots, the diluted dye was addedto the concentrated streptavidin with re-pipeting to mix, using a newpipet tip with each addition until the two solutions were completelycombined (adding the diluted dye to the concentrated enzyme favors theformation of the single dye bound species). The resulting 5 ml solutionwas then loaded into a 5 ml sample loop of an AKTAexplorer® 10 FPLCequipped with a MonoQ_10/100_GL ion exchange column. The sample waspurified using a linear gradient of 5% Buffer A to 50% Buffer B (5 mMTris HCl pH 7.4, 20% acetonitrile, 2 M NaCl) over 20 column volumes. 2ml fractions were collected while monitoring the wavelengths at 254,280, and 542 nm. A typical chromatogram is shown in FIG. 8. Thefractions containing the streptavidin complexes linked to a singlebis-biotin dye were pooled and concentrated using a 4 ml Amicon® Ultraspin concentrator (30K), and the sample was diluted to 4 mls in asolution of 5 mM Tris HCl pH 7.4 and subsequently reconcentrated toexchange the buffer.

Streptavidin Tetramer Stabilization

It was demonstrated that a single bis-biotin tag bound to a streptavidintetramer will stabilize the tetramer, even under the extreme conditionsof high temperature over an extended period followed by electrophoresisin the presence of a detergent. In one experiment, 27 μl of loadingbuffer was added to 3 μl of protein sample comprising a biotinylatedpolymerase bound to a streptavidin tetramer. The mixture was heated at90° C. for 20 minutes, and 10 μl of each of the resulting mixtures wasloaded onto an SDS-PAGE gel, and stained with SyPro® Ruby followingstandard protocols. FIG. 9 provides an image of one exemplaryhigh-throughput polymerase screening gel. The lanes numbered 1-11 eachcontain a different polymerase enzyme. Most are linked to a singlebiotin tag, but the two designated as 3 and 6 have bis-biotin tags. Thevarious bands are identified to the right of the gel. The lowest bandscontain only streptavidin monomers that were dissociated from tetramersduring the harsh treatment. The middle bands are polymerases that werealso dissociated from the streptavidin tetramers. The only two complexesthat remained intact are apparent as the two bands that run high on thegel. Each “supershifted” band comprises streptavidin bound to one of thebis-biotinylated polymerases. The fact that the supershifted bands showup only with the bis-biotinylated polymerase-streptavidin complexesindicates the superior stability of the bis-biotin strategy. In allother cases, the streptavidin tetramer and the singly biotinylatedpolymerase are denatured and separated.

Comparison of a Mono-Biotin Linkage to a Bis-Biotin Linkage in a SingleStreptavidin Complex

The higher stability of a bis-biotin linkage to streptavidin as comparedto a mono-biotin linkage was demonstrated using a complex comprising astreptavidin molecule having one dimer in the tetramer bound to abis-biotinylated fluorescent dye, and having the other dimer bound totwo individual mono-biotinylated compounds comprising multiplenucleotide polyphosphates, also termed “base clusters.” Examples of suchbase clusters, as well as complexes comprising streptavidin, dye, andbase clusters, are described in detail in U.S. patent application Ser.No. 13/767,619, filed Feb. 14, 2013, and incorporated herein byreference in its entirety for all purposes. The complex at aconcentration of 57 μM, was incubated with 10× excess of free biotin in5 mM Tris, pH 7.4. The free biotin served to occupy empty biotin-bindingsites on the streptavidin complex when there was dissociation of thebiotin moieties linked to the dye or base clusters. The timecourse wasrun for 900 minutes and 30 μl time points taken at 5, 10, 20, 40, 220,and 900 minutes were flash frozen. After the timecourse was run, thetime points were diluted to 500 μl in 5 mM Tris, pH 7.4. The sampleswere then injected into an analytica MonoQ™ anion-exchange column (1 mM)and analysis was performed according to manufacturer's instructions (GEHealthcare, Uppsala, Sweden) using Buffer A (5 mM Tris, pH 7.4; 20%acetonitrile (ACN)) and Buffer B (5 mM Tris, pH 7.4; 2 M NaCl; 20% ACN).The results showed that one of the mono-biotinylated base clustersdissociates readily, with a half-life of two hours, while thebis-biotinylated dye does not appreciably dissociate from the complex onthis timescale. Interestingly, the second base cluster also did notappreciably dissociate, and although not wishing to be bound by theory,this finding implies there is some negative cooperativity of binding ofthe two mono-biotinylated base clusters to the streptavidin complex,possibly due to charge-based and/or steric interferences.

What is claimed is:
 1. A composition comprising a protein comprising twobiotin ligase recognition sequences oriented in tandem at an N-terminalor C-terminal end of the protein, each biotin ligase recognitionsequence having a biotin moiety covalently linked thereto, wherein thetwo biotin ligase recognition sequences and the two biotins collectivelyconstitute a first bis-biotin tag; a solid support covalently coupled toa second bis-biotin tag; and a tetravalent biotin-binding agent to whichboth bis-biotin tags are bound.
 2. The composition of claim 1, whereinthe protein is a polymerase.
 3. The composition of claim 1, wherein thetwo biotin moieties in the first bis-biotin tag are separated by 20-60angstroms.
 4. The composition of claim 1, wherein the tetravalentbiotin-binding agent is a streptavidin tetramer.
 5. The composition ofclaim 4, wherein the streptavidin tetramer comprises a firststreptavidin dimer bound to both biotin moieties of the first bis-biotintag, and a second streptavidin dimer bound to both biotin moieties ofthe second bis-biotin tag.
 6. A method for immobilizing a protein, themethod comprising: a) providing a protein comprising two biotin ligaserecognition sequences oriented in tandem at an N-terminal or C-terminalend of the protein, each biotin ligase recognition sequence having abiotin moiety covalently linked thereto, wherein the two biotin ligaserecognition sequences and the two biotins collectively constitute afirst bis-biotin tag; b) covalently linking a solid support to a secondbis-biotin tag; c) binding the protein to a tetravalent biotin-bindingagent, thereby producing a first complex comprising the protein bound tothe tetravalent biotin-binding agent; and d) exposing the solid supportbearing the second bis-biotin tag to the first complex, therebyimmobilizing the protein on the solid support by producing a secondcomplex comprising the solid support bound to the first complex.
 7. Themethod of claim 6, further comprising isolating the first complex priorto said exposing the solid support.
 8. The method of claim 6, furthercomprising isolating the second complex.